In the western coast of Taiwan, the Portuguese oyster, Crassostrea angulata, is an important aquaculture species. However, the reason for this is unclear. Therefore, the information about the amount of genetic variation within and among population is important for further oyster broodstock management. In this study, we attempted to investigate genetic variations of the Portuguese oysters in Taiwan. We collected total 162 individuals from 13 locations around main island of Taiwan and its outer islands. A total of 110 variable sites were detected in 642~644 nucleotides in length, and the relative frequency of nucleotide alteration was determined to be 17.1 %. Among 162 specimens, 96 haplotypes were identified. The diversities among all sequences (dij) ranged from 0.001~0.079. The phylogenetic tree was reconstructed based on the Maximum likelihood and Neighbor-joining methods. The result showed that no obvious to distinguish the specimens into different populations through clustering analysis based on data of the mitochondrial noncoding region.